Multi-state Model-Based Identification of Cryptic Allosteric Sites on Human Serotonin Transporter

Serotonin transporter (SERT) plays a fundamental role
in taking
the synaptic cleft serotonin back to the presynaptic neuron. The discovery
of allosteric SERT modulators represents the next-generation medication
for psychiatric disorders such as depression. Here, based on the cryo-EM
structures of ibogaine in complex with SERT in distinct conformations,
the multiple functional structures of the transporter bound to serotonin,
including outward-open (OOholo), outward-occluded (OCholo), and inward-open (IOholo and IOholo′), were carefully characterized by induced-fit docking Gaussian-accelerated
molecular dynamics (IFD-GaMD) simulation and the free-energy landscape
analysis. Further MM/GBSA binding free energy, per-residue contribution,
and molecular interaction fingerprint calculations revealed the interaction
variations of serotonin with SERT in functional structures, which
confirmed the allostery of SERT during serotonin reuptake. Moreover,
five unique cryptic allosteric sites, which are druggable and capable
of targeting by small molecules, were identified on the characterized
multistate structures. These results provide structural and energetic
information for the molecular mechanism of serotonin reuptake and
will provide opportunities for the development of novel therapeutics
based on the identified new allosteric sites on SERT.